Forms of DNA

    DNA (Deoxyribonucleic Acid) is the genetic material found in almost all living organisms. While its most familiar structure is the double helix, DNA can exist in multiple structural forms, depending on conditions like hydration, ionic strength, and sequence.

Primary Forms of DNA

A. B-DNA (Standard Watson-Crick Form)

• Structure:
• Right-handed double helix.
• 10.5 base pairs per turn.
• Helix diameter: ~20 Å.
• Major and minor grooves (important for protein binding).
• Conditions:
• Most common in physiological conditions (92% relative humidity, low salt).
• Features:
• Anti-parallel strands.
• Base pairs perpendicular to the helix axis.

B. A-DNA (Dehydrated or Compact Form)

• Structure:
• Right-handed but shorter and wider than B-DNA.
• 11 base pairs per turn.
• Helix diameter: ~23 Å.
• Conditions:
• Forms under low humidity (75%) or high salt concentrations.
• Biological Role:
• Found in DNA-RNA hybrids (e.g., transcription bubbles).
• Adopted by some viral genomes.

C. Z-DNA (Left-Handed Zigzag Form)

• Structure:
• Left-handed double helix.
• 12 base pairs per turn.
• Zigzag sugar-phosphate backbone (hence "Z-DNA").
• Conditions:
• Favored by alternating purine-pyrimidine sequences (e.g., GCGCGC).
• Stabilized by high salt or negative supercoiling.
• Biological Role:
• Associated with gene regulation (e.g., promoter regions).
• May play a role in chromatin remodeling.

Other DNA Conformations

Triple-Stranded DNA (H-DNA)

• Structure:
• Forms when a third strand binds to B-DNA via Hoogsteen base pairing.
• Requires homopurine-homopyrimidine mirror repeats.
• Biological Role:
• May regulate transcription (e.g., in promoter regions).

E. Four-Stranded DNA (G-Quadruplex)

• Structure:
• Forms in guanine-rich regions (e.g., telomeres).
• Stabilized by K⁺ or Na⁺ ions.
• Biological Role:
• Telomere maintenance.
• Gene expression regulation (e.g., oncogene promoters).

F. Bent DNA

• Structure:
• DNA helix bends due to A-tracts (AAAA sequences).
• Biological Role:
• Important in nucleosome positioning and transcription factor binding.

G. Supercoiled DNA

• Structure:
• Over- or under-wound DNA (due to topoisomerase activity).
• Negative supercoiling: Favors transcription/replication.
• Positive supercoiling: Inhibits DNA processes.
• Biological Role:
• Essential for chromosome condensation and gene regulation.

Other Minor Forms

• C-DNA - Right-handed, occurs under certain ionic conditions (Li+ ions), intermediate between A and B
• D-DNA - Right-handed, 8 bp per turn, found in sequences rich in adenine and thymine
• E-DNA - Extended right-handed form observed under specific laboratory conditions
• P-DNA - Experimental form, overstretched DNA under mechanical stress (seen during single-molecule experiments).

Factors Influencing DNA Form

• Hydration level: Low water → A-DNA; High water → B-DNA
• Salt concentration: High salt (esp. Na⁺, Mg²⁺) promotes Z-DNA
• DNA sequence: GC-rich → Z-DNA; AT-rich → D-DNA
• Binding proteins: Certain proteins stabilize specific forms
• Supercoiling and torsional strain

Key Points :

DNA is structurally dynamic, and its form can vary with environment, sequence, and function.

• B-DNA: Default, biologically active form
• A-DNA: Seen in special conditions like low water or DNA-RNA hybrids
• Z-DNA: Involved in gene regulation and genome stability

MCQ's: 

1.      Which of the following is the most biologically prevalent form of DNA under physiological conditions?
a) A-DNA
b) B-DNA*
c) Z-DNA
d) H-DNA

2.      Z-DNA is characterized by:
a) Right-handed helix and 10.5 bp/turn
b) Left-handed helix and 12 bp/turn*
c) Triple-stranded structure
d) G-quadruplex formation

3.      The Meselson-Stahl experiment demonstrated:
a) DNA transcription
b) Semi-conservative DNA replication*
c) Protein synthesis
d) RNA splicing

4.      Which enzyme is responsible for introducing negative supercoils in DNA?
a) DNA polymerase
b) Helicase
c) Topoisomerase II (Gyrase)*
d) Ligase

5.      G-quadruplex DNA structures are stabilized by:
a) Mg²⁺ ions
b) K⁺ or Na⁺ ions*
c) Ca²⁺ ions
d) Zn²⁺ ions

6.      A researcher observes a DNA sequence with alternating purine-pyrimidine repeats (e.g., CGCGCG). Under high salt conditions, this sequence is most likely to adopt which conformation?
a) B-DNA
b) A-DNA
c) Z-DNA*
d) Triple-stranded H-DNA

7.      Which of the following statements about A-DNA is INCORRECT?
a) It has a wider diameter than B-DNA.
b) It forms under low humidity conditions.
c) It is left-handed like Z-DNA.*
d) It is observed in DNA-RNA hybrids.

8.      In a genome sequencing project, a region rich in guanine repeats (GGGTTAGGG) is identified. This region is most likely to form:
a) A cruciform structure
b) A G-quadruplex*
c) A triple helix
d) A bent DNA

9.      Negative supercoiling in bacterial DNA primarily facilitates:
a) Inhibition of transcription
b) Chromosome condensation
c) Strand separation during replication/transcription*
d) Prevention of mutation

10.  Which of the following techniques is MOST suitable for distinguishing between A-DNA and B-DNA?
a) SDS-PAGE
b) X-ray crystallography*
c) Western blotting
d) ELISA

11.  Match the following DNA forms with their biological significance:
I. Z-DNA
II. G-quadruplex
III. A-DNA
IV. Supercoiled DNA

A. Telomere maintenance
B. Transcription regulation in immune response genes
C. DNA-RNA hybrid stability
D. Chromosome packing in prokaryotes

Correct pairing:
a) I-B, II-A, III-C, IV-D*
b) I-C, II-B, III-A, IV-D
c) I-A, II-D, III-B, IV-C
d) I-D, II-C, III-A, IV-B

12.  A scientist treats a DNA sample with ethidium bromide and observes reduced electrophoretic mobility. This suggests:
a) Conversion to Z-DNA
b) Introduction of positive supercoils*
c) Formation of A-DNA
d) Cleavage by nucleases

13.  Which of the following sequences is MOST likely to induce DNA bending?
a) ATATAT
b) AAAAAA*
c) CGCGCG
d) GGGGGG

14.  In a study, deletion of a gene encoding topoisomerase I in E. coli leads to accumulation of highly supercoiled DNA. This indicates the enzyme normally:
a) Introduces negative supercoils
b) Relaxes negative supercoils*
c) Promotes Z-DNA formation
d) Stabilizes G-quadruplexes

15.  Which statement about Hoogsteen base pairing is TRUE?
a) It occurs in B-DNA.
b) It allows triple-helix (H-DNA) formation*
c) It stabilizes G-quadruplexes.
d) It requires left-handed helices.